open(my OUT,">$peptstr1")  or die  $!;
open(my IN,$genpept);
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my OUT and my IN are syntax errors and won't work.    You need to use scalar variables for that to work.    Also, you should always verify that the file opened correctly:

open my $OUT, '>', $peptstr1 or die "Cannot open '$peptstr1' because: 
+$!";
open my $IN,  '<', $genpept  or die "Cannot open '$genpept' because: $
+!";
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---

while (my $records = <IN>){
    #$i++;
    chomp $records;
    my @genpept;
    push @genpept,($records); 
    print"Processed infile record: $.\n";
    foreach(@genpept){
        print "$_";
    }
}
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You don't print to the OUT filehandle so everything is going to STDOUT and not your file.